moleditpy 3.0.0a2__tar.gz → 3.0.0a3__tar.gz

{moleditpy-3.0.0a2 → moleditpy-3.0.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a2
+Version: 3.0.0a3
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -711,7 +711,7 @@ Dynamic: license-file
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
 ![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
@@ -834,6 +834,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a3}/README.md

@@ -7,7 +7,7 @@
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
 ![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
@@ -130,6 +130,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a3}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "MoleditPy"
 
-version = "3.0.0a2"
+version = "3.0.0a3"
 
 license = {file = "LICENSE"}
 

{moleditpy-3.0.0a2 → moleditpy-3.0.0a3}/src/MoleditPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: MoleditPy
-Version: 3.0.0a2
+Version: 3.0.0a3
 Summary: A cross-platform, simple, and intuitive molecular structure editor built in Python. It allows 2D molecular drawing and 3D structure visualization. It supports exporting structure files for input to DFT calculation software.
 Author-email: HiroYokoyama <titech.yoko.hiro@gmail.com>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -711,7 +711,7 @@ Dynamic: license-file
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![Build Status](https://github.com/HiroYokoyama/python_molecular_editor/actions/workflows/tests.yml/badge.svg)](https://github.com/HiroYokoyama/python_molecular_editor/actions)
 ![Core Logic Coverage](https://img.shields.io/badge/core_logic_coverage-80%25-green)
-![Overall Coverage](https://img.shields.io/badge/coverage-63.83%25-green)
+![Overall Coverage](https://img.shields.io/badge/coverage-64%25-green)
 ![GUI Status](https://img.shields.io/badge/GUI-Manually_Verified-blue)
 ![Pylint Score](https://img.shields.io/badge/pylint-8.93%2F10-brightgreen)
 [![PyPI Downloads](https://static.pepy.tech/personalized-badge/moleditpy?period=total&units=INTERNATIONAL_SYSTEM&left_color=BLACK&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/moleditpy)
@@ -834,6 +834,7 @@ moleditpy
   * **GUI and 2D Drawing (PyQt6):** The editor is built on a `QGraphicsScene`, where custom `AtomItem` and `BondItem` objects are interactively manipulated. The Undo/Redo feature is implemented by serializing the application state.
   * **Chemical Calculations (RDKit / Open Babel):** RDKit is used to generate molecule objects from 2D data, perform 3D coordinate generation, and calculate properties. Open Babel serves as a fallback for 3D conversion. All heavy computations are run on a separate `QThread` to keep the GUI responsive.
   * **3D Visualization (PyVista / pyvistaqt):** 3D rendering is achieved by generating PyVista meshes (spheres and cylinders) from RDKit conformer coordinates. A custom `vtkInteractorStyle` enables direct drag-and-drop editing of atoms in the 3D view.
+  * **Modular Architecture:** The codebase is organized into dedicated packages for `core` logic, `ui` components, and `utils`. The main application logic is decomposed into reusable mixins, ensuring long-term maintainability and easier verification.
 
 ## License
 

moleditpy-3.0.0a3/src/MoleditPy.egg-info/SOURCES.txt

@@ -0,0 +1,86 @@
+LICENSE
+README.md
+pyproject.toml
+src/MoleditPy.egg-info/PKG-INFO
+src/MoleditPy.egg-info/SOURCES.txt
+src/MoleditPy.egg-info/dependency_links.txt
+src/MoleditPy.egg-info/entry_points.txt
+src/MoleditPy.egg-info/requires.txt
+src/MoleditPy.egg-info/top_level.txt
+src/moleditpy/__init__.py
+src/moleditpy/__main__.py
+src/moleditpy/main.py
+src/moleditpy.egg-info/PKG-INFO
+src/moleditpy.egg-info/SOURCES.txt
+src/moleditpy.egg-info/dependency_links.txt
+src/moleditpy.egg-info/entry_points.txt
+src/moleditpy.egg-info/requires.txt
+src/moleditpy.egg-info/top_level.txt
+src/moleditpy/assets/file_icon.ico
+src/moleditpy/assets/icon.icns
+src/moleditpy/assets/icon.ico
+src/moleditpy/assets/icon.png
+src/moleditpy/core/__init__.py
+src/moleditpy/core/mol_geometry.py
+src/moleditpy/core/molecular_data.py
+src/moleditpy/modules/__init__.py
+src/moleditpy/plugins/__init__.py
+src/moleditpy/plugins/plugin_interface.py
+src/moleditpy/plugins/plugin_manager.py
+src/moleditpy/plugins/plugin_manager_window.py
+src/moleditpy/ui/__init__.py
+src/moleditpy/ui/about_dialog.py
+src/moleditpy/ui/align_plane_dialog.py
+src/moleditpy/ui/alignment_dialog.py
+src/moleditpy/ui/analysis_window.py
+src/moleditpy/ui/angle_dialog.py
+src/moleditpy/ui/app_state.py
+src/moleditpy/ui/atom_item.py
+src/moleditpy/ui/bond_item.py
+src/moleditpy/ui/bond_length_dialog.py
+src/moleditpy/ui/calculation_worker.py
+src/moleditpy/ui/color_settings_dialog.py
+src/moleditpy/ui/compute_engine.py
+src/moleditpy/ui/compute_logic.py
+src/moleditpy/ui/constrained_optimization_dialog.py
+src/moleditpy/ui/custom_interactor_style.py
+src/moleditpy/ui/custom_qt_interactor.py
+src/moleditpy/ui/dialog_3d_picking_mixin.py
+src/moleditpy/ui/dialog_logic.py
+src/moleditpy/ui/dialog_manager.py
+src/moleditpy/ui/dihedral_dialog.py
+src/moleditpy/ui/edit_3d.py
+src/moleditpy/ui/edit_3d_logic.py
+src/moleditpy/ui/edit_actions.py
+src/moleditpy/ui/edit_actions_logic.py
+src/moleditpy/ui/export_logic.py
+src/moleditpy/ui/main_window.py
+src/moleditpy/ui/main_window_init.py
+src/moleditpy/ui/mirror_dialog.py
+src/moleditpy/ui/molecular_parsers.py
+src/moleditpy/ui/molecular_scene_handler.py
+src/moleditpy/ui/molecule_scene.py
+src/moleditpy/ui/move_group_dialog.py
+src/moleditpy/ui/periodic_table_dialog.py
+src/moleditpy/ui/planarize_dialog.py
+src/moleditpy/ui/project_io.py
+src/moleditpy/ui/settings_dialog.py
+src/moleditpy/ui/sip_isdeleted_safe.py
+src/moleditpy/ui/string_importers.py
+src/moleditpy/ui/template_preview_item.py
+src/moleditpy/ui/template_preview_view.py
+src/moleditpy/ui/translation_dialog.py
+src/moleditpy/ui/ui_manager.py
+src/moleditpy/ui/user_template_dialog.py
+src/moleditpy/ui/view_3d_logic.py
+src/moleditpy/ui/view_loaders.py
+src/moleditpy/ui/zoomable_view.py
+src/moleditpy/ui/settings_tabs/__init__.py
+src/moleditpy/ui/settings_tabs/settings_2d_tab.py
+src/moleditpy/ui/settings_tabs/settings_3d_tabs.py
+src/moleditpy/ui/settings_tabs/settings_other_tab.py
+src/moleditpy/ui/settings_tabs/settings_tab_base.py
+src/moleditpy/utils/__init__.py
+src/moleditpy/utils/constants.py
+src/moleditpy/utils/sip_isdeleted_safe.py
+src/moleditpy/utils/system_utils.py

moleditpy-3.0.0a3/src/moleditpy/__init__.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+MoleditPy — A Python-based molecular editing software
+
+Author: Hiromichi Yokoyama
+License: GPL-3.0 license
+Repo: https://github.com/HiroYokoyama/python_molecular_editor
+DOI: 10.5281/zenodo.17268532
+"""
+
+"""Top-level package for moleditpy."""
+
+import importlib.util
+
+try:
+    OBABEL_AVAILABLE = importlib.util.find_spec("openbabel") is not None
+except ImportError:
+    OBABEL_AVAILABLE = False

{moleditpy-3.0.0a2/src/moleditpy/modules → moleditpy-3.0.0a3/src/moleditpy/core}/mol_geometry.py

@@ -18,6 +18,8 @@ submodules without circular dependencies.
 """
 
 import numpy as np
+import math
+from collections import deque
 
 # ------------------------------------------------------------------
 # Primitive geometry helpers
@@ -437,3 +439,148 @@ def identify_valence_problems(atoms_data, bonds_data):
             problem_atom_ids.append(atom_id)
 
     return problem_atom_ids
+
+
+def optimize_2d_coords(mol):
+    """Generate 2D coordinates using RDKit and return a map of (x, y) tuples."""
+    from rdkit.Chem import AllChem
+
+    AllChem.Compute2DCoords(mol)
+    conf = mol.GetConformer()
+    new_positions = {}
+    for rdkit_atom in mol.GetAtoms():
+        if rdkit_atom.HasProp("_original_atom_id"):
+            original_id = rdkit_atom.GetIntProp("_original_atom_id")
+            pos = conf.GetAtomPosition(rdkit_atom.GetIdx())
+            new_positions[original_id] = (pos.x, pos.y)
+    return new_positions
+
+
+def calculate_best_fit_plane_projection(centered_positions, normal, centroid):
+    """Project centered points orthogonally onto the plane defined by normal and centroid."""
+    projections = centered_positions - np.outer(
+        np.dot(centered_positions, normal), normal
+    )
+    return projections + centroid
+
+
+def rotate_2d_points(points_map, center_x, center_y, angle_degrees):
+    """Rotate 2D points (atom_id -> (x, y)) around a center."""
+    rad = math.radians(angle_degrees)
+    cos_a = math.cos(rad)
+    sin_a = math.sin(rad)
+    new_positions = {}
+    for atom_id, (x, y) in points_map.items():
+        dx = x - center_x
+        dy = y - center_y
+        new_dx = dx * cos_a - dy * sin_a
+        new_dy = dx * sin_a + dy * cos_a
+        new_positions[atom_id] = (center_x + new_dx, center_y + new_dy)
+    return new_positions
+
+
+def resolve_2d_overlaps(
+    atom_ids,
+    positions_map,
+    adjacency_list,
+    overlap_threshold=0.5,
+    move_distance=20,
+    has_bond_check_func=None,
+):
+    """Detect and resolve overlapping atom groups in 2D.
+
+    Returns list of (atom_ids_set, translation_vector_tuple).
+    """
+    overlapping_pairs = []
+    ids_list = list(atom_ids)
+    for i in range(len(ids_list)):
+        for j in range(i + 1, len(ids_list)):
+            id1 = ids_list[i]
+            id2 = ids_list[j]
+
+            # Skip directly bonded pairs
+            if has_bond_check_func and has_bond_check_func(id1, id2):
+                continue
+
+            p1 = positions_map[id1]
+            p2 = positions_map[id2]
+            dist = math.sqrt((p1[0] - p2[0]) ** 2 + (p1[1] - p2[1]) ** 2)
+            if dist < overlap_threshold:
+                overlapping_pairs.append((id1, id2))
+
+    if not overlapping_pairs:
+        return []
+
+    # Union-Find for overlap groups
+    parent = {aid: aid for aid in atom_ids}
+
+    def find_set(aid):
+        if parent[aid] == aid:
+            return aid
+        parent[aid] = find_set(parent[aid])
+        return parent[aid]
+
+    def unite_sets(aid1, aid2):
+        root1 = find_set(aid1)
+        root2 = find_set(aid2)
+        if root1 != root2:
+            parent[root2] = root1
+
+    for id1, id2 in overlapping_pairs:
+        unite_sets(id1, id2)
+
+    groups_by_root = {}
+    for aid in atom_ids:
+        root = find_set(aid)
+        groups_by_root.setdefault(root, []).append(aid)
+
+    move_operations = []
+    processed_roots = set()
+
+    for root_id, group_ids in groups_by_root.items():
+        if root_id in processed_roots or len(group_ids) < 2:
+            continue
+        processed_roots.add(root_id)
+
+        # Split into fragments via BFS
+        fragments = []
+        visited = set()
+        group_set = set(group_ids)
+        for aid in group_ids:
+            if aid not in visited:
+                frag = set()
+                q = deque([aid])
+                visited.add(aid)
+                frag.add(aid)
+                while q:
+                    curr = q.popleft()
+                    for neighbor in adjacency_list.get(curr, []):
+                        if neighbor in group_set and neighbor not in visited:
+                            visited.add(neighbor)
+                            frag.add(neighbor)
+                            q.append(neighbor)
+                fragments.append(frag)
+
+        if len(fragments) < 2:
+            continue
+
+        # Find representative pair
+        rep_id1, rep_id2 = None, None
+        for i1, i2 in overlapping_pairs:
+            if find_set(i1) == root_id:
+                rep_id1, rep_id2 = i1, i2
+                break
+
+        if not rep_id1:
+            continue
+
+        frag1 = next((f for f in fragments if rep_id1 in f), None)
+        frag2 = next((f for f in fragments if rep_id2 in f), None)
+        if not frag1 or not frag2 or frag1 == frag2:
+            continue
+
+        ids_to_move = frag1 if rep_id1 > rep_id2 else frag2
+        # Move vector (-move_distance, move_distance)
+        move_operations.append((ids_to_move, (-move_distance, move_distance)))
+
+    return move_operations

{moleditpy-3.0.0a2/src/moleditpy/modules → moleditpy-3.0.0a3/src/moleditpy/core}/molecular_data.py

@@ -1,4 +1,3 @@
-import logging
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
@@ -11,13 +10,23 @@ Repo: https://github.com/HiroYokoyama/python_molecular_editor
 DOI: 10.5281/zenodo.17268532
 """
 
+import logging
 from rdkit import Chem
-from PyQt6.QtCore import QPointF
 
 try:
-    from .constants import ANGSTROM_PER_PIXEL
+    from ..utils.constants import ANGSTROM_PER_PIXEL
 except ImportError:
-    from modules.constants import ANGSTROM_PER_PIXEL
+    from moleditpy.utils.constants import ANGSTROM_PER_PIXEL
+
+
+class PointTuple(tuple):
+    """Backward-compatible tuple that allows .x() and .y() access like QPointF."""
+
+    def x(self):
+        return self[0]
+
+    def y(self):
+        return self[1]
 
 
 class MolecularData:
@@ -29,9 +38,15 @@ class MolecularData:
 
     def add_atom(self, symbol, pos, charge=0, radical=0):
         atom_id = self._next_atom_id
+        # Internalize position as raw floats to decouple from UI types (QPointF)
+        if hasattr(pos, "x") and hasattr(pos, "y"):
+            raw_pos = PointTuple((float(pos.x()), float(pos.y())))
+        else:
+            raw_pos = PointTuple((float(pos[0]), float(pos[1])))
+
         self.atoms[atom_id] = {
             "symbol": symbol,
-            "pos": pos,
+            "pos": raw_pos,
             "item": None,
             "charge": charge,
             "radical": radical,
@@ -40,6 +55,16 @@ class MolecularData:
         self._next_atom_id += 1
         return atom_id
 
+    def set_atom_pos(self, atom_id, pos):
+        """Update atom position using raw floats or QPointF."""
+        if atom_id in self.atoms:
+            if hasattr(pos, "x") and hasattr(pos, "y"):
+                self.atoms[atom_id]["pos"] = PointTuple(
+                    (float(pos.x()), float(pos.y()))
+                )
+            else:
+                self.atoms[atom_id]["pos"] = PointTuple((float(pos[0]), float(pos[1])))
+
     def add_bond(self, id1, id2, order=1, stereo=0):
         # For stereo bonds, do not sort because ID order determines direction.
         # For non-stereo bonds, sort to normalize the key.
@@ -68,16 +93,11 @@ class MolecularData:
             # Safely get neighbors before deleting the atom's own entry
             neighbors = self.adjacency_list.get(atom_id, [])
             for neighbor_id in neighbors:
-                try:
-                    if (
-                        neighbor_id in self.adjacency_list
-                        and atom_id in self.adjacency_list[neighbor_id]
-                    ):
-                        self.adjacency_list[neighbor_id].remove(atom_id)
-                except (ValueError, KeyError, TypeError) as e:
-                    logging.debug(
-                        f"Suppressed exception: {e}"
-                    )  # Ignore adjacency list inconsistencies during atom removal
+                if (
+                    neighbor_id in self.adjacency_list
+                    and atom_id in self.adjacency_list[neighbor_id]
+                ):
+                    self.adjacency_list[neighbor_id].remove(atom_id)
 
             # Now, safely delete the atom's own entry from the adjacency list
             if atom_id in self.adjacency_list:
@@ -87,14 +107,9 @@ class MolecularData:
                 del self.atoms[atom_id]
 
             # Remove bonds involving this atom
-            try:
-                bonds_to_remove = [key for key in self.bonds if atom_id in key]
-                for key in bonds_to_remove:
-                    del self.bonds[key]
-            except (RuntimeError, KeyError) as e:
-                logging.debug(
-                    f"Suppressed exception: {e}"
-                )  # Ignore mutation issues during batch bond removal
+            bonds_to_remove = [key for key in self.bonds if atom_id in key]
+            for key in bonds_to_remove:
+                self.bonds.pop(key, None)
 
     def remove_bond(self, id1, id2):
         # Look for directional stereo bonds (forward/reverse) and normalized non-stereo bond keys.
@@ -105,16 +120,11 @@ class MolecularData:
             key_to_remove = (id2, id1)
 
         if key_to_remove:
-            try:
-                if id1 in self.adjacency_list and id2 in self.adjacency_list[id1]:
-                    self.adjacency_list[id1].remove(id2)
-                if id2 in self.adjacency_list and id1 in self.adjacency_list[id2]:
-                    self.adjacency_list[id2].remove(id1)
-                del self.bonds[key_to_remove]
-            except (ValueError, KeyError) as e:
-                logging.debug(
-                    f"Suppressed exception: {e}"
-                )  # Ignore if bond already removed or inconsistent
+            if id1 in self.adjacency_list and id2 in self.adjacency_list[id1]:
+                self.adjacency_list[id1].remove(id2)
+            if id2 in self.adjacency_list and id1 in self.adjacency_list[id2]:
+                self.adjacency_list[id2].remove(id1)
+            self.bonds.pop(key_to_remove, None)
 
     def to_rdkit_mol(self, use_2d_stereo=True):
         """
@@ -125,7 +135,7 @@ class MolecularData:
             return None
         mol = Chem.RWMol()
 
-        # --- Step 1: atoms ---
+        # atoms
         atom_id_to_idx_map = {}
         for atom_id, data in self.atoms.items():
             try:
@@ -140,7 +150,7 @@ class MolecularData:
             idx = mol.AddAtom(atom)
             atom_id_to_idx_map[atom_id] = idx
 
-        # --- Step 2: save bonds & stereo info (label info is kept here) ---
+        # save bonds & stereo info (label info is kept here)
         bond_stereo_info = {}  # bond_idx -> {'type': int, 'atom_ids': (id1,id2), 'bond_data': bond_data}
         for (id1, id2), bond_data in self.bonds.items():
             if id1 not in atom_id_to_idx_map or id2 not in atom_id_to_idx_map:
@@ -165,7 +175,7 @@ class MolecularData:
                     "bond_data": bond_data,
                 }
 
-        # --- Step 3: sanitize ---
+        # sanitize
         final_mol = mol.GetMol()
         try:
             Chem.SanitizeMol(final_mol)
@@ -173,7 +183,7 @@ class MolecularData:
             # Sanitization failure: return None to trigger manual MOL block fallback
             return None
 
-        # --- Step 4: add 2D conformer ---
+        # add 2D conformer
         # Convert from scene pixels to angstroms when creating RDKit conformer.
         conf = Chem.Conformer(final_mol.GetNumAtoms())
         conf.Set3D(False)
@@ -182,14 +192,19 @@ class MolecularData:
                 idx = atom_id_to_idx_map[atom_id]
                 pos = data.get("pos")
                 if pos:
-                    ax = pos.x() * ANGSTROM_PER_PIXEL
-                    ay = (
-                        -pos.y() * ANGSTROM_PER_PIXEL
-                    )  # Invert Y-coordinate (screen coordinates -> chemical coordinates)
+                    # pos may be a tuple (x, y) or a QPointF (from old state deserialization)
+                    if hasattr(pos, "x") and hasattr(pos, "y"):
+                        ax = pos.x() * ANGSTROM_PER_PIXEL
+                        ay = -pos.y() * ANGSTROM_PER_PIXEL
+                    elif isinstance(pos, (list, tuple)) and len(pos) >= 2:
+                        ax = pos[0] * ANGSTROM_PER_PIXEL
+                        ay = -pos[1] * ANGSTROM_PER_PIXEL
+                    else:
+                        continue
                     conf.SetAtomPosition(idx, (ax, ay, 0.0))
         final_mol.AddConformer(conf)
 
-        # --- Step 5: Stereochemistry setting prioritizing E/Z labels ---
+        # Stereochemistry setting prioritizing E/Z labels ---
         # First, record bonds with E/Z labels
         ez_labeled_bonds = set()
         for bond_idx, info in bond_stereo_info.items():
@@ -223,7 +238,7 @@ class MolecularData:
                     return nbr.GetIdx()
             return None
 
-        # --- Step 6: Overwrite based on labels (E/Z has highest priority) ---
+        # Overwrite based on labels (E/Z has highest priority) ---
         for bond_idx, info in bond_stereo_info.items():
             stereo_type = info["type"]
             bond = final_mol.GetBondWithIdx(bond_idx)
@@ -280,7 +295,7 @@ class MolecularData:
                 if b2 is not None:
                     b2.SetBondDir(Chem.BondDir.NONE)
 
-        # Step 7: Finalization (cache update + stereochemistry reassignment)
+        # Finalization (cache update + stereochemistry reassignment)
         final_mol.UpdatePropertyCache(strict=False)
 
         # During 3D conversion (use_2d_stereo=False), apply force=True if E/Z labels exist
@@ -347,18 +362,17 @@ class MolecularData:
             positions = []
             for aidx in a_ring:
                 item = rdkit_idx_to_item.get(aidx)
-                if item:
-                    try:
-                        positions.append(item.pos())
-                    except (AttributeError, RuntimeError) as e:
-                        logging.debug(f"Suppressed exception: {e}")
+                if item and hasattr(item, "pos"):
+                    pos = item.pos()
+                    if pos is not None:
+                        positions.append(pos)
 
             if not positions:
                 continue
 
             center_x = sum(p.x() for p in positions) / len(positions)
             center_y = sum(p.y() for p in positions) / len(positions)
-            ring_center = QPointF(center_x, center_y)
+            ring_center = (center_x, center_y)  # Use tuple (x, y) instead of QPointF
 
             # Update all bonds in this ring
             for bidx in b_ring:
@@ -378,9 +392,9 @@ class MolecularData:
             try:
                 return Chem.MolToMolBlock(mol, includeStereo=True)
             except (RuntimeError, ValueError, TypeError) as e:
-                logging.debug(
-                    f"Suppressed exception: {e}"
-                )  # Suppress errors during RDKit MolBlock generation
+                logging.warning(
+                    f"RDKit MolBlock generation failed: {e}"
+                )  # Fallback to manual MolBlock generation if RDKit fails
 
         if not self.atoms:
             return None
@@ -390,8 +404,17 @@ class MolecularData:
         mol_block += f"{num_atoms:3d}{num_bonds:3d}  0  0  0  0  0  0  0  0999 V2000\n"
         for old_id, atom in self.atoms.items():
             # Convert scene pixel coordinates to angstroms when emitting MOL block
-            x_px = atom["item"].pos().x()
-            y_px = -atom["item"].pos().y()
+            pos = atom.get("pos")
+            if not pos:
+                continue
+
+            if hasattr(pos, "x") and hasattr(pos, "y"):
+                x_px, y_px = pos.x(), -pos.y()
+            elif isinstance(pos, (list, tuple)) and len(pos) >= 2:
+                x_px, y_px = pos[0], -pos[1]
+            else:
+                continue
+
             x, y = x_px * ANGSTROM_PER_PIXEL, y_px * ANGSTROM_PER_PIXEL
             z, symbol = 0.0, atom["symbol"]
             charge = atom.get("charge", 0)
@@ -425,3 +448,44 @@ class MolecularData:
 
         mol_block += "M  END\n"
         return mol_block
+
+    def to_template_dict(self, name, version="1.0", application_version=""):
+        """Convert current structure to a dictionary for template storage."""
+        import datetime
+
+        atoms_data = []
+        for atom_id, atom_info in self.atoms.items():
+            pos = atom_info["pos"]
+            # pos is guaranteed to be a tuple (x, y) due to internal caching in add_atom/set_atom_pos
+            atoms_data.append(
+                {
+                    "id": atom_id,
+                    "symbol": atom_info["symbol"],
+                    "x": pos[0],
+                    "y": pos[1],
+                    "charge": atom_info.get("charge", 0),
+                    "radical": atom_info.get("radical", 0),
+                }
+            )
+
+        bonds_data = []
+        for (id1, id2), bond_info in self.bonds.items():
+            bonds_data.append(
+                {
+                    "atom1": id1,
+                    "atom2": id2,
+                    "order": bond_info["order"],
+                    "stereo": bond_info.get("stereo", 0),
+                }
+            )
+
+        return {
+            "format": "PME Template",
+            "version": version,
+            "application": "MoleditPy",
+            "application_version": application_version,
+            "name": name,
+            "created": str(datetime.datetime.now()),
+            "atoms": atoms_data,
+            "bonds": bonds_data,
+        }